Pyrimidine nucleoside phosphorylase(PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. The enzyme has two structure states: non-active opened structure and active...Pyrimidine nucleoside phosphorylase(PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. The enzyme has two structure states: non-active opened structure and active closed structure. During change from non-active opened structure to active closed structure, the protein loop connecting domain α to domain α/β becomes bent remarkablely, which results in two domains closed up, and binding pocket reduce obviously. Setting about from the inactive-open X-ray structure, applying the method of molecular dynamic simulation, putting the ligand in the active-pocket, we carry out a dynamic simulation in the CVFF force-field for the entire system. The structures obstained are more approximately to the active-close X-ray structures, it proves that the rigid movement of the domains is arouse by the inducing effect of the ligand molecules.展开更多
文摘Pyrimidine nucleoside phosphorylase(PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. The enzyme has two structure states: non-active opened structure and active closed structure. During change from non-active opened structure to active closed structure, the protein loop connecting domain α to domain α/β becomes bent remarkablely, which results in two domains closed up, and binding pocket reduce obviously. Setting about from the inactive-open X-ray structure, applying the method of molecular dynamic simulation, putting the ligand in the active-pocket, we carry out a dynamic simulation in the CVFF force-field for the entire system. The structures obstained are more approximately to the active-close X-ray structures, it proves that the rigid movement of the domains is arouse by the inducing effect of the ligand molecules.
